\HeaderA{getLocOrfs}{A function to obtain ORFs for the ScISI}{getLocOrfs}
\keyword{datagen}{getLocOrfs}
\begin{Description}\relax
This function takes a list of bi-partite graph incidence matrices as
well as a vector of GO nodes, and for each protein complex of each
bi-partite graph, finds those constituent member proteins which are
annotated to each GO node.
\end{Description}
\begin{Usage}
\begin{verbatim}
getLocOrfs(imList, goNode, pathToSave = NULL, name = NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{imList}] A list of bi-partite graph incidence matrices
\item[\code{goNode}] A character vector of GO ID's
\item[\code{pathToSave}] A character denoting where to save the resultant data
\item[\code{name}] The name by which the resulting R-object as well as the file
will be named
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Currently, this function will take a protein complex and find those
constituent protein members which have also been annotated to the user
specified GO ID. For instance, the GO ID "" is the nucleus ID. This
function will find all proteins within an interactome which has been
annotated with the ID "". NB - if n GO ID is supplied, the
function returns n different interactomes, each is has proteins
uniquely annotated with each GO ID.
\end{Details}
\begin{Value}
The return value is a list of lists of lists:

1. The top level list contains entries named by each GO ID
2. The second tier level contains entries after each entry of imList
3. The third tier level contains three entries:
i.   A bi-partite graph incidence matrix which only has protein
complexes restricted to the respective GO ID annotation
ii.  A bi-partite graph incidence matrix which only has protein
complexes listed in (i) but contains all the original
proteins
iii. A vector of proportions. We look at the column sums of (i)
divided by the column sums fo (ii). This gives the ratio of
proteins which are annotated by the GO ID over all other
proteins in that complex    

\begin{ldescription}
\item[\code{restrictedOrfsComp}] A bi-partite graph incidence matrix which
only has protein complexes restricted to the respective GO ID
annotation
\item[\code{restrictedOrfsOnly}] A bi-partite graph incidence matrix which
only has protein complexes listed in (i) but contains all the
original proteins
\item[\code{ratio}] A vector of proportions. We look at the column sums of
(i) divided by the column sums fo (ii). This gives the ratio of
proteins which are annotated by the GO ID over all other proteins in
that complex
\end{ldescription}
\end{Value}
\begin{Author}\relax
TC
\end{Author}
\begin{References}\relax
\textasciitilde{}put references to the literature/web site here \textasciitilde{}
\end{References}

